7QF9

Crystal structure of PDE6D bound to HRas peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.1 M Tris pH 8.5, 8% w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.626	α = 90
b = 82.789	β = 90
c = 112.467	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2019-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	56.234	99.8	1	16.9	6.4		24377

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			0.772

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5TB5	1.95	56.234	24329	1197	99.75	0.233	0.2295	0.2993	41.591

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.543			2.041		-1.499

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.034
r_dihedral_angle_3_deg	17.526
r_dihedral_angle_4_deg	15.96
r_lrange_it	7.551
r_lrange_other	7.547
r_dihedral_angle_1_deg	7.101
r_scangle_it	5.633
r_scangle_other	5.631
r_mcangle_it	4.318
r_mcangle_other	4.316
r_scbond_it	3.822
r_scbond_other	3.821
r_mcbond_it	3.359
r_mcbond_other	3.359
r_angle_other_deg	1.538
r_angle_refined_deg	1.165
r_symmetry_nbd_other	0.222
r_nbd_other	0.212
r_nbd_refined	0.181
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.144
r_ncsr_local_group_1	0.138
r_symmetry_nbd_refined	0.133
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.04
r_xyhbond_nbd_other	0.039
r_symmetry_xyhbond_nbd_other	0.01
r_bond_other_d	0.003
r_bond_refined_d	0.002
r_gen_planes_refined	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2440
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing